The papillomaviruses are associated with naturally occurring carcinomas in a variety of species, including man. There are now 41 human papillomaviruses (HPVs) which have been identified in man. Six of these, HPV-6, HPV-11, HPV-16, HPV-18, HPV-31 and HPV-33, have been associated with human genital tract lesions. HPV-6, HPV-11, and HPV-31 have been found to be associated with a high percentage of benign genital warts, including cervical flat warts and dysplasia. HPV-16, HPV-18, and HPV-31 were each cloned directly from cervical carcinoma biopsy specimens and have been found in a high percentage of cervical carcinomas. We have previously screened a series of human carcinoma cell lines for the presence of human papillomavirus DNA sequences using HPV-6, HPV-11, HPV-16, and HPV-18 DNA probes. Six of eight cell lines which had been derived from human cervical carcinoma lines were found to contain integrated HPV DNA sequences. In five of these lines, HPV-specific polyadenylated RNA species could be identified. Two of the cell lines contained integrated HPV-16 DNA and in each of these cell lines the genomes were transcriptionally active. Genomic clones have been made from these HPV-16 positive lines and have been characterized. In the SiHa cell line in which only a single copy of the HPV-16 genome is integrated, the cellular flanking sequences have been sequenced. Integration has occurred in the E2 ORF of the HPV-16 genome. We have characterized a conditional enhancer in the control region of the HPV-16 genome and have shown that the E2 gene of HPV-16 encodes a transcriptional transactivating function that induces this enhancer element.